In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing.
Aneuploidy
Chinese Spring
Chromosome deletion
Computational
Monosomic
Nullisomic
Trisomic
Journal
Plant methods
ISSN: 1746-4811
Titre abrégé: Plant Methods
Pays: England
ID NLM: 101245798
Informations de publication
Date de publication:
2020
2020
Historique:
received:
31
10
2019
accepted:
23
03
2020
entrez:
14
4
2020
pubmed:
14
4
2020
medline:
14
4
2020
Statut:
epublish
Résumé
Short read sequencing technologies, such as genotyping-by-sequencing (GBS), have been utilized in genetic mapping, marker development, and population genomic studies. High-throughput and multiplexing capability coupled with low cost make GBS an appropriate tool for molecular research. Here, we present the application of GBS to characterize wheat aneuploid stocks and detect chromosomal aberrations including aneuploidy and chromosomal deletions. These aneuploids are an important resource that have been used in wheat genetics and genomics studies to localize genes, determine physical positions, and develop chromosome bin maps. Using GBS, we mapped sequence reads and quantified read coverage across chromosome bins. Using this approach, we confirmed known deletions and aneuploid stocks. In addition, we were also able to fully characterize these stocks and to identify several novel deletions and aneuploids. With this knowledge and a quick detection tool at our disposal, we can easily isolate these deletions and aneuploids into distinct lines. We envision this tool to replace the intensive cytogenetics techniques, such as C-banding, and fluorescent- and genomic-in situ hybridization to accurately detect chromosome dosage and segmental deletions in wheat genetic stocks as well as other crop species.
Sections du résumé
BACKGROUND
BACKGROUND
Short read sequencing technologies, such as genotyping-by-sequencing (GBS), have been utilized in genetic mapping, marker development, and population genomic studies. High-throughput and multiplexing capability coupled with low cost make GBS an appropriate tool for molecular research. Here, we present the application of GBS to characterize wheat aneuploid stocks and detect chromosomal aberrations including aneuploidy and chromosomal deletions. These aneuploids are an important resource that have been used in wheat genetics and genomics studies to localize genes, determine physical positions, and develop chromosome bin maps.
RESULTS
RESULTS
Using GBS, we mapped sequence reads and quantified read coverage across chromosome bins. Using this approach, we confirmed known deletions and aneuploid stocks. In addition, we were also able to fully characterize these stocks and to identify several novel deletions and aneuploids. With this knowledge and a quick detection tool at our disposal, we can easily isolate these deletions and aneuploids into distinct lines.
CONCLUSION
CONCLUSIONS
We envision this tool to replace the intensive cytogenetics techniques, such as C-banding, and fluorescent- and genomic-in situ hybridization to accurately detect chromosome dosage and segmental deletions in wheat genetic stocks as well as other crop species.
Identifiants
pubmed: 32280361
doi: 10.1186/s13007-020-00588-3
pii: 588
pmc: PMC7137276
doi:
Types de publication
Journal Article
Langues
eng
Pagination
45Informations de copyright
© The Author(s) 2020.
Déclaration de conflit d'intérêts
Competing interestsAuthors declare no competing interests.
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